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Chen L, Ren Y, Lin J, Liu X, Pang X, Lin J. Acidithiobacillus caldus sulfur oxidation model based on transcriptome analysis between the wild type and sulfur oxygenase reductase defective mutant. PLoS One 2012; 7:e39470. [PMID: 22984393 PMCID: PMC3440390 DOI: 10.1371/journal.pone.0039470] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 05/21/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Acidithiobacillus caldus (A. caldus) is widely used in bio-leaching. It gains energy and electrons from oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs) for carbon dioxide fixation and growth. Genomic analyses suggest that its sulfur oxidation system involves a truncated sulfur oxidation (Sox) system (omitting SoxCD), non-Sox sulfur oxidation system similar to the sulfur oxidation in A. ferrooxidans, and sulfur oxygenase reductase (SOR). The complexity of the sulfur oxidation system of A. caldus generates a big obstacle on the research of its sulfur oxidation mechanism. However, the development of genetic manipulation method for A. caldus in recent years provides powerful tools for constructing genetic mutants to study the sulfur oxidation system. RESULTS An A. caldus mutant lacking the sulfur oxygenase reductase gene (sor) was created and its growth abilities were measured in media using elemental sulfur (S(0)) and tetrathionate (K(2)S(4)O(6)) as the substrates, respectively. Then, comparative transcriptome analysis (microarrays and real-time quantitative PCR) of the wild type and the Δsor mutant in S(0) and K(2)S(4)O(6) media were employed to detect the differentially expressed genes involved in sulfur oxidation. SOR was concluded to oxidize the cytoplasmic elemental sulfur, but could not couple the sulfur oxidation with the electron transfer chain or substrate-level phosphorylation. Other elemental sulfur oxidation pathways including sulfur diooxygenase (SDO) and heterodisulfide reductase (HDR), the truncated Sox pathway, and the S(4)I pathway for hydrolysis of tetrathionate and oxidation of thiosulfate in A. caldus are proposed according to expression patterns of sulfur oxidation genes and growth abilities of the wild type and the mutant in different substrates media. CONCLUSION An integrated sulfur oxidation model with various sulfur oxidation pathways of A. caldus is proposed and the features of this model are summarized.
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Affiliation(s)
- Linxu Chen
- State Key Lab of Microbial Technology, Shandong University, Jinan, China
| | - Yilin Ren
- School of Life Science, Shandong Normal University, Jinan, China
| | - Jianqun Lin
- State Key Lab of Microbial Technology, Shandong University, Jinan, China
| | - Xiangmei Liu
- State Key Lab of Microbial Technology, Shandong University, Jinan, China
| | - Xin Pang
- State Key Lab of Microbial Technology, Shandong University, Jinan, China
| | - Jianqiang Lin
- State Key Lab of Microbial Technology, Shandong University, Jinan, China
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202
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Hao L, Liu X, Wang H, Lin J, Pang X, Lin J. Detection and validation of a small broad-host-range plasmid pBBR1MCS-2 for use in genetic manipulation of the extremely acidophilic Acidithiobacillus sp. J Microbiol Methods 2012; 90:309-14. [DOI: 10.1016/j.mimet.2012.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 06/05/2012] [Accepted: 06/05/2012] [Indexed: 11/29/2022]
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203
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Jaramillo ML, Abanto M, Quispe RL, Calderón J, del Valle LJ, Talledo M, Ramírez P. Cloning, expression and bioinformatics analysis of ATP sulfurylase from Acidithiobacillus ferrooxidans ATCC 23270 in Escherichia coli. Bioinformation 2012; 8:695-704. [PMID: 23055613 PMCID: PMC3449377 DOI: 10.6026/97320630008695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 11/23/2022] Open
Abstract
Molecular studies of enzymes involved in sulfite oxidation in Acidithiobacillus ferrooxidans have not yet been developed, especially in the ATP sulfurylase (ATPS) of these acidophilus tiobacilli that have importance in biomining. This enzyme synthesizes ATP and sulfate from adenosine phosphosulfate (APS) and pyrophosphate (PPi), final stage of the sulfite oxidation by these organisms in order to obtain energy. The atpS gene (1674 bp) encoding the ATPS from Acidithiobacillus ferrooxidans ATCC 23270 was amplified using PCR, cloned in the pET101-TOPO plasmid, sequenced and expressed in Escherichia coli obtaining a 63.5 kDa ATPS recombinant protein according to SDS-PAGE analysis. The bioinformatics and phylogenetic analyses determined that the ATPS from A. ferrooxidans presents ATP sulfurylase (ATS) and APS kinase (ASK) domains similar to ATPS of Aquifex aeolicus, probably of a more ancestral origin. Enzyme activity towards ATP formation was determined by quantification of ATP formed from E. coli cell extracts, using a bioluminescence assay based on light emission by the luciferase enzyme. Our results demonstrate that the recombinant ATP sulfurylase from A. ferrooxidans presents an enzymatic activity for the formation of ATP and sulfate, and possibly is a bifunctional enzyme due to its high homology to the ASK domain from A. aeolicus and true kinases.
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Affiliation(s)
- Michael L Jaramillo
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
| | - Michel Abanto
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
| | - Ruth L Quispe
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
| | - Julio Calderón
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
| | - Luís J del Valle
- Centre díEnginyeria Biotecnologica i Molecular (CEBIM), Departament díEnginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Miguel Talledo
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
| | - Pablo Ramírez
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
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204
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Denkmann K, Grein F, Zigann R, Siemen A, Bergmann J, van Helmont S, Nicolai A, Pereira IAC, Dahl C. Thiosulfate dehydrogenase: a widespread unusual acidophilicc-type cytochrome. Environ Microbiol 2012; 14:2673-88. [DOI: 10.1111/j.1462-2920.2012.02820.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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205
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Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation. Appl Environ Microbiol 2012; 78:6545-9. [PMID: 22773644 DOI: 10.1128/aem.01349-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Except for several conspicuous cases, very little is known about sulfur oxidizers living in natural freshwater environments. Sulfuricella denitrificans skB26 is a psychrotolerant sulfur oxidizer recently isolated from a freshwater lake as a representative of a new genus in the class Betaproteobacteria. In this study, an approximately 3.2-Mb draft genome sequence of strain skB26 was obtained. In the draft genome, consisting of 23 contigs, a single rRNA operon, 43 tRNA genes, and 3,133 coding sequences were identified. The identified genes include those required for sulfur oxidation, denitrification, and carbon fixation. Comparative proteomic analysis was conducted to assess cold adaptation mechanisms of this organism. From cells grown at 22°C and 5°C, proteins were extracted for analysis by nano-liquid chromatography-electrospray ionization-tandem mass spectrometry. In the cells cultured at 5°C, relative abundances of ribosomal proteins, cold shock proteins, and DEAD/DEAH box RNA helicases were increased in comparison to those at 22°C. These results suggest that maintenance of proper translation is critical for growth under low-temperature conditions, similar to the case for other cold-adapted prokaryotes.
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206
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Expression, purification and molecular modeling of another HdrC from Acidithiobacillus ferrooxidans which binds only one [4Fe-4S] cluster. Curr Microbiol 2012; 65:416-23. [PMID: 22760247 DOI: 10.1007/s00284-012-0173-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
Abstract
The heterodisulfide reductase complex HdrABC from Acidithiobacillus ferrooxidans was predicted to have novel features that work in reverse to catalyse the sulfane sulfur of GSnH species (n > 1) into sulfite in sulfur oxidation. There are two different highly upregulated genes potentially encoding the HdrC subunit in A. ferrooxidans grown in sulfur-containing medium. An HdrC containing iron-sulfur cluster from A. ferrooxidans corresponding to one of the genes had been expressed and biophysically characterized. Comparatively, here we report the cloning, expression, and characterization of another HdrC from A. ferrooxidans. This HdrC was expressed in inclusion bodies in all conditions tested. This purified HdrC displayed brown color and contained the [4Fe-4S] cluster confirmed by the UV-scanning and EPR spectra. This HdrC owned two identical motifs (Cx(2)Cx(2)Cx(3)C) including total of eight cysteine residues for [4Fe-4S] cluster binding. To our surprise, the site-directed mutagenesis results of these eight residues revealed that respective removal of the sulfhydryl group of Cys73, Cys76, Cys79, and Cys37 resulted in the cluster loss, but those of Cys27, Cys30, Cys33, and Cys83 had no influence, which demonstrated that this HdrC bound only one cluster, and it might be responsible for causing the HdrABC in A. ferrooxidans working in reverse. Molecular modeling results also supported the above results and showed that this cluster was ligated by Cys73, Cys76, and Cys79 in one motif and Cys37, however, in another motif.
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207
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Dopson M, Johnson DB. Biodiversity, metabolism and applications of acidophilic sulfur-metabolizing microorganisms. Environ Microbiol 2012; 14:2620-31. [PMID: 22510111 DOI: 10.1111/j.1462-2920.2012.02749.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extremely acidic, sulfur-rich environments can be natural, such as solfatara fields in geothermal and volcanic areas, or anthropogenic, such as acid mine drainage waters. Many species of acidophilic bacteria and archaea are known to be involved in redox transformations of sulfur, using elemental sulfur and inorganic sulfur compounds as electron donors or acceptors in reactions involving between one and eight electrons. This minireview describes the nature and origins of acidic, sulfur-rich environments, the biodiversity of sulfur-metabolizing acidophiles, and how sulfur is metabolized and assimilated by acidophiles under aerobic and anaerobic conditions. Finally, existing and developing technologies that harness the abilities of sulfur-oxidizing and sulfate-reducing acidophiles to extract and capture metals, and to remediate sulfur-polluted waste waters are outlined.
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Affiliation(s)
- Mark Dopson
- School of Natural Sciences, Linnaeus University, Kalmar, Sweden
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208
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Kozubal MA, Macur RE, Jay ZJ, Beam JP, Malfatti SA, Tringe SG, Kocar BD, Borch T, Inskeep WP. Microbial iron cycling in acidic geothermal springs of yellowstone national park: integrating molecular surveys, geochemical processes, and isolation of novel fe-active microorganisms. Front Microbiol 2012; 3:109. [PMID: 22470372 PMCID: PMC3312321 DOI: 10.3389/fmicb.2012.00109] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 03/05/2012] [Indexed: 12/02/2022] Open
Abstract
Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats in Yellowstone National Park. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 88°C and pH 2.4 to 3.6. All iron oxide mats exhibited high diversity of crenarchaeal sequences from the Sulfolobales, Thermoproteales, and Desulfurococcales. The predominant Sulfolobales sequences were highly similar to Metallosphaera yellowstonensis str. MK1, previously isolated from one of these sites. Other groups of archaea were consistently associated with different types of iron oxide mats, including undescribed members of the phyla Thaumarchaeota and Euryarchaeota. Bacterial sequences were dominated by relatives of Hydrogenobaculum spp. above 65–70°C, but increased in diversity below 60°C. Cultivation of relevant iron-oxidizing and iron-reducing microbial isolates included Sulfolobus str. MK3, Sulfobacillus str. MK2, Acidicaldus str. MK6, and a new candidate genus in the Sulfolobales referred to as Sulfolobales str. MK5. Strains MK3 and MK5 are capable of oxidizing ferrous iron autotrophically, while strain MK2 oxidizes iron mixotrophically. Similar rates of iron oxidation were measured for M. yellowstonensis str. MK1 and Sulfolobales str. MK5. Biomineralized phases of ferric iron varied among cultures and field sites, and included ferric oxyhydroxides, K-jarosite, goethite, hematite, and scorodite depending on geochemical conditions. Strains MK5 and MK6 are capable of reducing ferric iron under anaerobic conditions with complex carbon sources. The combination of geochemical and molecular data as well as physiological observations of isolates suggests that the community structure of acidic Fe mats is linked with Fe cycling across temperatures ranging from 53 to 88°C.
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Affiliation(s)
- Mark A Kozubal
- Thermal Biology Institute, Montana State University Bozeman, MT, USA
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209
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Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Foster B, Sun H, Ivanova N, Pati A, D'haeseleer P, Woyke T, Kyrpides NC. Complete genome sequence of Thioalkalivibrio sp. K90mix. Stand Genomic Sci 2011; 5:341-55. [PMID: 22675584 PMCID: PMC3368412 DOI: 10.4056/sigs.2315092] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method. Here we report the complete genome sequence of strain K90mix and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from wastewater and gas streams.
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Affiliation(s)
- Gerard Muyzer
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Dimitry Y. Sorokin
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | | | - Alla Lapidus
- Joint Genome Institute, Walnut Creek, California, USA
| | - Brian Foster
- Joint Genome Institute, Walnut Creek, California, USA
| | - Hui Sun
- Joint Genome Institute, Walnut Creek, California, USA
| | | | - Amrita Pati
- Joint Genome Institute, Walnut Creek, California, USA
| | | | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, California, USA
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210
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Development of a markerless gene replacement system for Acidithiobacillus ferrooxidans and construction of a pfkB mutant. Appl Environ Microbiol 2011; 78:1826-35. [PMID: 22210219 DOI: 10.1128/aem.07230-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The extremely acidophilic, chemolithoautotrophic Acidithiobacillus ferrooxidans is an important bioleaching bacterium of great value in the metallurgical industry and environmental protection. In this report, a mutagenesis system based on the homing endonuclease I-SceI was developed to produce targeted, unmarked gene deletions in the strain A. ferrooxidans ATCC 23270. A targeted phosphofructokinase (PFK) gene (pfkB) mutant of A. ferrooxidans ATCC 23270 was constructed by homologous recombination and identified by PCR with specific primers as well as Southern blot analysis. This potential pfkB gene (AFE_1807) was also characterized by expression in PFK-deficient Escherichia coli cells, and heteroexpression of the PFKB protein demonstrated that it had functional PFK activity, though it was significantly lower (about 800-fold) than that of phosphofructokinase-2 (PFK-B) expressed by the pfkB gene from E. coli K-12. The function of the potential PFKB protein in A. ferrooxidans was demonstrated by comparing the properties of the pfkB mutant with those of the wild type. The pfkB mutant strain displayed a relatively reduced growth capacity in S(0) medium (0.5% [wt/vol] elemental sulfur in 9K basal salts solution adjusted to pH 3.0 with H(2)SO(4)), but the mutation did not completely prevent A. ferrooxidans from assimilating exogenous glucose. The transcriptional analysis of some related genes in central carbohydrate metabolism in the wild-type and mutant strains with or without supplementation of glucose was carried out by quantitative reverse transcription-PCR. This report suggests that the markerless mutagenesis strategy could serve as a model for functional studies of other genes of interest from A. ferrooxidans and multiple mutations could be made in a single A. ferrooxidans strain.
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211
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Mi S, Song J, Lin J, Che Y, Zheng H, Lin J. Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation. J Microbiol 2011; 49:890-901. [DOI: 10.1007/s12275-011-1099-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 07/27/2011] [Indexed: 12/23/2022]
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212
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Valdes J, Ossandon F, Quatrini R, Dopson M, Holmes DS. Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus. J Bacteriol 2011; 193:7003-4. [PMID: 22123759 PMCID: PMC3232857 DOI: 10.1128/jb.06281-11] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 10/03/2011] [Indexed: 11/20/2022] Open
Abstract
Acidithiobacillus thiooxidans is a mesophilic, extremely acidophilic, chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation of sulfur and inorganic sulfur compounds. Here we present the draft genome sequence of A. thiooxidans ATCC 19377, which has allowed the identification of genes for survival and colonization of extremely acidic environments.
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Affiliation(s)
- Jorge Valdes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Francisco Ossandon
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Raquel Quatrini
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Mark Dopson
- School of Natural Sciences, Linnaeus University, SE-391 82 Kalmar, Sweden
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
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213
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Kucera J, Bouchal P, Cerna H, Potesil D, Janiczek O, Zdrahal Z, Mandl M. Kinetics of anaerobic elemental sulfur oxidation by ferric iron in Acidithiobacillus ferrooxidans and protein identification by comparative 2-DE-MS/MS. Antonie van Leeuwenhoek 2011; 101:561-73. [PMID: 22057833 DOI: 10.1007/s10482-011-9670-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/27/2011] [Indexed: 11/25/2022]
Abstract
Elemental sulfur oxidation by ferric iron in Acidithiobacillus ferrooxidans was investigated. The apparent Michaelis constant for ferric iron was 18.6 mM. An absence of anaerobic ferric iron reduction ability was observed in bacteria maintained on elemental sulfur for an extended period of time. Upon transition from ferrous iron to elemental sulfur medium, the cells exhibited similar kinetic characteristics of ferric iron reduction under anaerobic conditions to those of cells that were originally maintained on ferrous iron. Nevertheless, a total loss of anaerobic ferric iron reduction ability after the sixth passage in elemental sulfur medium was demonstrated. The first proteomic screening of total cell lysates of anaerobically incubated bacteria resulted in the detection of 1599 protein spots in the master two-dimensional electrophoresis gel. A set of 59 more abundant and 49 less abundant protein spots that changed their protein abundances in an anaerobiosis-dependent manner was identified and compared to iron- and sulfur-grown cells, respectively. Proteomic analysis detected a significant increase in abundance under anoxic conditions of electron transporters, such as rusticyanin and cytochrome c(552), involved in the ferrous iron oxidation pathway. Therefore we suggest the incorporation of rus-operon encoded proteins in the anaerobic respiration pathway. Two sulfur metabolism proteins were identified, pyridine nucleotide-disulfide oxidoreductase and sulfide-quinone reductase. The important transcription regulator, ferric uptake regulation protein, was anaerobically more abundant. The anaerobic expression of several proteins involved in cell envelope formation indicated a gradual adaptation to elemental sulfur oxidation.
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Affiliation(s)
- Jiri Kucera
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
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214
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Bonnefoy V, Holmes DS. Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments. Environ Microbiol 2011; 14:1597-611. [DOI: 10.1111/j.1462-2920.2011.02626.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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215
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Bird LJ, Bonnefoy V, Newman DK. Bioenergetic challenges of microbial iron metabolisms. Trends Microbiol 2011; 19:330-40. [DOI: 10.1016/j.tim.2011.05.001] [Citation(s) in RCA: 264] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 04/30/2011] [Accepted: 05/03/2011] [Indexed: 11/24/2022]
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216
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Ossa D, Oliveira R, Murakami M, Vicentini R, Costa-Filho A, Alexandrino F, Ottoboni L, Garcia O. Expression, purification and spectroscopic analysis of an HdrC: An iron–sulfur cluster-containing protein from Acidithiobacillus ferrooxidans. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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217
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Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Clum A, Ivanova N, Pati A, d'Haeseleer P, Woyke T, Kyrpides NC. Complete genome sequence of "Thioalkalivibrio sulfidophilus" HL-EbGr7. Stand Genomic Sci 2011; 4:23-35. [PMID: 21475584 PMCID: PMC3072093 DOI: 10.4056/sigs.1483693] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
"Thioalkalivibrio sulfidophilus" HL-EbGr7 is an obligately chemolithoautotrophic, haloalkaliphilic sulfur-oxidizing bacterium (SOB) belonging to the Gammaproteobacteria. The strain was found to predominate a full-scale bioreactor, removing sulfide from biogas. Here we report the complete genome sequence of strain HL-EbGr7 and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from bio- and industrial waste gases.
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218
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Mangold S, Valdés J, Holmes DS, Dopson M. Sulfur metabolism in the extreme acidophile acidithiobacillus caldus. Front Microbiol 2011; 2:17. [PMID: 21687411 PMCID: PMC3109338 DOI: 10.3389/fmicb.2011.00017] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/25/2011] [Indexed: 12/20/2022] Open
Abstract
Given the challenges to life at low pH, an analysis of inorganic sulfur compound (ISC) oxidation was initiated in the chemolithoautotrophic extremophile Acidithiobacillus caldus. A. caldus is able to metabolize elemental sulfur and a broad range of ISCs. It has been implicated in the production of environmentally damaging acidic solutions as well as participating in industrial bioleaching operations where it forms part of microbial consortia used for the recovery of metal ions. Based upon the recently published A. caldus type strain genome sequence, a bioinformatic reconstruction of elemental sulfur and ISC metabolism predicted genes included: sulfide-quinone reductase (sqr), tetrathionate hydrolase (tth), two sox gene clusters potentially involved in thiosulfate oxidation (soxABXYZ), sulfur oxygenase reductase (sor), and various electron transport components. RNA transcript profiles by semi quantitative reverse transcription PCR suggested up-regulation of sox genes in the presence of tetrathionate. Extensive gel based proteomic comparisons of total soluble and membrane enriched protein fractions during growth on elemental sulfur and tetrathionate identified differential protein levels from the two Sox clusters as well as several chaperone and stress proteins up-regulated in the presence of elemental sulfur. Proteomics results also suggested the involvement of heterodisulfide reductase (HdrABC) in A. caldus ISC metabolism. A putative new function of Hdr in acidophiles is discussed. Additional proteomic analysis evaluated protein expression differences between cells grown attached to solid, elemental sulfur versus planktonic cells. This study has provided insights into sulfur metabolism of this acidophilic chemolithotroph and gene expression during attachment to solid elemental sulfur.
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Affiliation(s)
| | - Jorge Valdés
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para VidaSantiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para VidaSantiago, Chile
- Departamento de Ciencias Biologicas, Andrés Bello UniversitySantiago, Chile
| | - Mark Dopson
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para VidaSantiago, Chile
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219
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Amouric A, Brochier-Armanet C, Johnson DB, Bonnefoy V, Hallberg KB. Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways. Microbiology (Reading) 2011; 157:111-122. [DOI: 10.1099/mic.0.044537-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Autotrophic acidophilic iron- and sulfur-oxidizing bacteria of the genus Acidithiobacillus constitute a heterogeneous taxon encompassing a high degree of diversity at the phylogenetic and genetic levels, though currently only two species are recognized (Acidithiobacillus ferrooxidans and Acidithiobacillus ferrivorans). One of the major functional disparities concerns the biochemical mechanisms of iron and sulfur oxidation, with discrepancies reported in the literature concerning the genes and proteins involved in these processes. These include two types of high-potential iron–sulfur proteins (HiPIPs): (i) Iro, which has been described as the iron oxidase; and (ii) Hip, which has been proposed to be involved in the electron transfer between sulfur compounds and oxygen. In addition, two rusticyanins have been described: (i) rusticyanin A, encoded by the rusA gene and belonging to the well-characterized rus operon, which plays a central role in the iron respiratory chain; and (ii) rusticyanin B, a protein to which no function has yet been ascribed. Data from a multilocus sequence analysis of 21 strains of Fe(II)-oxidizing acidithiobacilli obtained from public and private collections using five phylogenetic markers showed that these strains could be divided into four monophyletic groups. These divisions correlated not only with levels of genomic DNA hybridization and phenotypic differences among the strains, but also with the types of rusticyanin and HiPIPs that they harbour. Taken together, the data indicate that Fe(II)-oxidizing acidithiobacilli comprise at least four distinct taxa, all of which are able to oxidize both ferrous iron and sulfur, and suggest that different iron oxidation pathways have evolved in these closely related bacteria.
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Affiliation(s)
- Agnès Amouric
- Laboratoire de Chimie Bactérienne, UPR-CNRS 9043, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, 31 chemin Joseph Aiguier, 13009, Marseille, France
| | - Céline Brochier-Armanet
- Laboratoire de Chimie Bactérienne, UPR-CNRS 9043, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, 31 chemin Joseph Aiguier, 13009, Marseille, France
| | - D. Barrie Johnson
- School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Violaine Bonnefoy
- Laboratoire de Chimie Bactérienne, UPR-CNRS 9043, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, 31 chemin Joseph Aiguier, 13009, Marseille, France
| | - Kevin B. Hallberg
- School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
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Chang HY, Ahn Y, Pace LA, Lin MT, Lin YH, Gennis RB. The diheme cytochrome c(4) from Vibrio cholerae is a natural electron donor to the respiratory cbb(3) oxygen reductase. Biochemistry 2010; 49:7494-503. [PMID: 20715760 DOI: 10.1021/bi1004574] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The respiratory chain of Vibrio cholerae contains three bd-type quinol oxygen reductases as well as one cbb(3) oxygen reductase. The cbb(3) oxygen reductase has been previously isolated and characterized; however, the natural mobile electron donor(s) that shuttles electrons between the bc(1) complex and the cbb(3) oxygen reductase is not known. The most likely candidates are the diheme cytochrome c(4) and monoheme cytochrome c(5), which have been previously shown to be present in the periplasm of aerobically grown cultures of V. cholerae. Both cytochromes c(4) and c(5) from V. cholerae have been cloned and expressed heterologously in Escherichia coli. It is shown that reduced cytochrome c(4) is a substrate for the purified cbb(3) oxygen reductase and can support steady state oxygen reductase activity of at least 300 e(-1)/s. In contrast, reduced cytochrome c(5) is not a good substrate for the cbb(3) oxygen reductase. Surprisingly, the dependence of the oxygen reductase activity on the concentration of cytochrome c(4) does not exhibit saturation. Global spectroscopic analysis of the time course of the oxidation of cytochrome c(4) indicates that the apparent lack of saturation is due to the strong dependence of K(M) and V(max) on the concentration of oxidized cytochrome c(4). Whether this is an artifact of the in vitro assay or has physiological significance remains unknown. Cyclic voltammetry was used to determine that the midpoint potentials of the two hemes in cytochrome c(4) are 240 and 340 mV (vs standard hydrogen electrode), similar to the electrochemical properties of other c(4)-type cytochromes. Genomic analysis shows a strong correlation between the presence of a c(4)-type cytochrome and a cbb(3) oxygen reductase within the beta- and gamma-proteobacterial clades, suggesting that cytochrome c(4) is the likely natural electron donor to the cbb(3) oxygen reductases within these organisms. These would include the beta-proteobacteria Neisseria meningitidis and Neisseria gonnorhoeae, in which the cbb(3) oxygen reductases are the only terminal oxidases in their respiratory chains, and the gamma-proteobacterium Pseudomonas stutzeri.
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Affiliation(s)
- Hsin-Yang Chang
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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Dinarieva TY, Zhuravleva AE, Pavlenko OA, Tsaplina IA, Netrusov AI. Ferrous iron oxidation in moderately thermophilic acidophile Sulfobacillus sibiricus N1T. Can J Microbiol 2010; 56:803-8. [DOI: 10.1139/w10-063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The iron-oxidizing system of a moderately thermophilic, extremely acidophilic, gram-positive mixotroph, Sulfobacillus sibiricus N1T, was studied by spectroscopic, high-performance liquid chromatography and inhibitory analyses. Hemes B, A, and O were detected in membranes of S. sibiricus N1T. It is proposed that the electron transport chain from Fe2+ to O2 is terminated by 2 physiological oxidases: aa3-type cytochrome, which dominates in the early-exponential phase of growth, and bo3-type cytochrome, whose role in iron oxidation becomes more prominent upon growth of the culture. Both oxidases were sensitive to cyanide and azide. Cytochrome aa3 was more sensitive to cyanide and azide, with Ki values of 4.1 and 2.5 µmol·L–1, respectively, compared with Ki values for cytochrome bo3, which were 9.5 µmol·L–1 for cyanide and 7.0 µmol·L–1 for azide. This is the first evidence for the participation of a bo3-type oxidase in ferrous iron oxidation. The respiratory chain of the mixotroph contains, in addition to the 2 terminal oxidases, a membrane-bound cytochrome b573.
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Affiliation(s)
- Tatiana Y. Dinarieva
- Department of Microbiology, Faculty of Biology, Moscow State University, 1/12 Lenin’s Hills, Moscow 119992, Russian Federation
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, 7/2 pr. 60-letiya Oktyabrya, Moscow 117312, Russian Federation
| | - Anna E. Zhuravleva
- Department of Microbiology, Faculty of Biology, Moscow State University, 1/12 Lenin’s Hills, Moscow 119992, Russian Federation
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, 7/2 pr. 60-letiya Oktyabrya, Moscow 117312, Russian Federation
| | - Oksana A. Pavlenko
- Department of Microbiology, Faculty of Biology, Moscow State University, 1/12 Lenin’s Hills, Moscow 119992, Russian Federation
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, 7/2 pr. 60-letiya Oktyabrya, Moscow 117312, Russian Federation
| | - Iraida A. Tsaplina
- Department of Microbiology, Faculty of Biology, Moscow State University, 1/12 Lenin’s Hills, Moscow 119992, Russian Federation
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, 7/2 pr. 60-letiya Oktyabrya, Moscow 117312, Russian Federation
| | - Alexander I. Netrusov
- Department of Microbiology, Faculty of Biology, Moscow State University, 1/12 Lenin’s Hills, Moscow 119992, Russian Federation
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, 7/2 pr. 60-letiya Oktyabrya, Moscow 117312, Russian Federation
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Overexpression of Rusticyanin in Acidithiobacillus ferrooxidans ATCC19859 Increased Fe(II) Oxidation Activity. Curr Microbiol 2010; 62:320-4. [DOI: 10.1007/s00284-010-9708-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 06/28/2010] [Indexed: 10/19/2022]
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Affiliation(s)
- Dianne K. Newman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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